Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal Pathogen Scedosporium aurantiacum.

Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and ß-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on "Scedosporium/Pseudallescheria Infections" and "Fungal Respiratory Infections in Cystic Fibrosis".

Phialemoniopsis, a new genus of Sordariomycetes, and new species of Phialemonium and Lecythophora.

In molecular studies involving numerous clinical isolates of the genera Acremonium, Phialemonium and Lecytophora some of them could not be identified. To clarify the phylogenetic relationships among these fungi and other related taxa, we performed a polyphasic study based on a detailed morphological study and on the analysis of sequences of four loci: the internal transcribed spacer regions, the D1/D2 domains of the 28S rRNA, actin and ß-tubulin genes. The combination of the resulting data let us propose the new genus Phialemoniopsis to accommodate the opportunistic fungi Phialemonium curvatum and Sarcopodium oculorum and two new species, Phialemoniopsis cornearis and Phialemoniopsis pluriloculosa. The taxonomy of Phialemoniopsis has not been completely resolved, however, remaining incertae sedis within the Sordariomycetes. In addition, the new species Lecythophora luteorubra, Lecythophora cateniformis and Phialemonium globosum are described and the species Acremonium atrogriseum and Taifanglania inflata are transferred to the genus Phialemonium. Lecythophora and Phialemonium are currently monophyletic genera of the families Coniochaetaceae (Coniochaetales) and Cephalothecaceae (Sordariales) respectively, according to our results. Tables summarizing key morphological features to distinguish the current species of Lecythophora, Phialemonium and Phialemoniopsis are provided.

Polyphasic analysis of Purpureocillium lilacinum isolates from different origins and proposal of the new species Purpureocillium lavendulum.

Purpureocillium is a genus recently proposed to accommodate Paecilomyces lilacinus, a well studied species that has biotechnological properties and an ability to cause human infections. Since contradictory data have been reported on the intraspecific genetic variability of P. lilacinum, we have carried out a polyphasic study of a set of clinical and environmental isolates of this species. Detailed morphological examination and sequence analysis of four different loci, including the ribosomal internal transcribed spacer, the domains D1 and D2 of the 28S rDNA, EF-1a and the largest subunit of RNA polymerase II (rpb1), showed that P. lilacinum formed a well supported phylogenetic clade with low intraspecific variability. The new species Purpureocillium lavendulum, which has vinaceous colonies similar to those of P. lilacinum, is proposed. It is characterized by the lack of growth at 35 C, the production of a yellow diffusible pigment and by subglobose or limoniform conidia.

Genotyping of Scedosporium species: a review of molecular approaches.

Scedosporium species are increasingly encountered opportunistic fungal pathogens not only in immunocompromised patients but are also significant primary pathogens in immunocompetent individuals. The environmental reservoir of these fungi is uncertain and the epidemiology and mode of transmission are not well-defined. Conventional phenotypic methods are of limited use for epidemiological purposes since they are insensitive and inadequately discriminatory. Molecular techniques not only enable accurate phylogenetic delineation of species but also provide the means for rapid, reliable genotyping of strains for epidemiological and population genetic studies. This review discusses the methods that have been applied for genotyping of these increasingly important pathogens.